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A four-component Ugi reaction is described for the stereoselective synthesis of novel C-N atropisomeric peptide analogues. Using this approach, a combination of simple, readily available starting materials ( ortho -substituted anilines, aldehydes, carboxylic acids and isocyanides) could be combined to access complex products possessing both central and axial chirality in up to 92% yield and >95 : 5 d.r. Variation of the reaction temperature enabled the development of stereodivergent reactions capable of selectively targeting either diastereoisomer of a desired product from a single set of starting materials with high levels of stereocontrol. Detailed experimental and computational studies have been performed to probe the reaction mechanism and stereochemical outcome of these reactions. Preliminary studies show that novel atropisomeric scaffolds prepared using this method display inhibitory activity against M. tuberculosis with a significant difference in activity observed between different atropisomers., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Atropisomeric N -chloroamides were efficiently accessed by electrophilic halogenation of ortho -substituted secondary anilides. The stereodynamics of atropisomerism in these novel scaffolds was interrogated by detailed experimental and computational studies, revealing that racemization is correlated with amide isomerization. The stereoelectronic nature of the amide was shown to significantly influence racemization rates, with potentially important implications for other C-N atropisomeric scaffolds.

Rendering a common ligand scaffold anionic and then pairing it with a chiral cation represents an alternative strategy for developing enantioselective versions of challenging transformations, as has been recently demonstrated in the enantioselective borylation of arenes using a quinine-derived chiral cation. A significant barrier to the further generalization of this approach is the lack of understanding of the specific interactions involved between the cation, ligand, and substrate, given the complexity of the system. We have embarked on a detailed computational study probing the mechanism, the key noncovalent interactions involved, and potential origin of selectivity for the desymmetrizing borylation of two distinct classes of substrate. We describe a deconstructive, stepwise approach to tackling this complex challenge, which involves building up a detailed understanding of the pairwise components of the nominally three component system before combining together into the full 263-atom reactive complex. This approach has revealed substantial differences in the noncovalent interactions occurring at the stereodetermining transition state for C-H oxidative addition to iridium for the two substrate classes. Each substrate engages in a unique mixture of diverse interactions, a testament to the rich and privileged structure of the cinchona alkaloid-derived chiral cations. Throughout the study, experimental support is provided, and this culminates in the discovery that prochiral phosphine oxide substrates, lacking hydrogen bond donor functionality, can also give very encouraging levels of enantioselectivity, potentially through direct interactions with the chiral cation. We envisage that the findings in this study will spur further developments in using chiral cations as controllers in asymmetric transition-metal catalysis., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Catalytic enantioselective Minisci reactions have recently been developed but all instances so far utilize α-amino radical coupling partners. We report a substantial evolution of the enantioselective Minisci reaction that enables α-hydroxy radicals to be used, providing valuable enantioenriched secondary alcohol products. This is achieved through the direct oxidative coupling of two C-H bonds on simple alcohol and pyridine partners through a hydrogen atom transfer (HAT)-driven approach: a challenging process to achieve due to the numerous side reactions that can occur. Our approach is highly regioselective as well as highly enantioselective. Dicumyl peroxide, upon irradiation with 390 nm light, serves as both HAT reagent and oxidant whilst selectivity is controlled by use of a chiral phosphoric acid catalyst. Computational and experimental evidence provide mechanistic insight as to the origin of selectivity, revealing a stereodetermining deprotonation step distinct from the analogous reaction of amide-containing substrates., (© 2022 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

The use of machine learning techniques in computational chemistry has gained significant momentum since large molecular databases are now readily available. Predictions of molecular properties using machine learning have advantages over the traditional quantum mechanics calculations because they can be cheaper computationally without losing the accuracy. We present a new extrapolatable and explainable molecular representation based on bonds, angles and dihedrals that can be used to train machine learning models. The trained models can accurately predict the electronic energy and the free energy of small organic molecules with atom types C, H N and O, with a mean absolute error of 1.2 kcal mol -1 . The models can be extrapolated to larger organic molecules with an average error of less than 3.7 kcal mol -1 for 10 or fewer heavy atoms, which represent a chemical space two orders of magnitude larger. The rapid energy predictions of multiple molecules, up to 7 times faster than previous ML models of similar accuracy, has been achieved by sampling geometries around the potential energy surface minima. Therefore, the input geometries do not have to be located precisely on the minima and we show that accurate density functional theory energy predictions can be made from force-field optimised geometries with a mean absolute error 2.5 kcal mol -1 ., Competing Interests: There are no conflicts of interest., (This journal is © The Royal Society of Chemistry.)

Gold(I)-catalyzed nucleophilic allylations of pyridinium and quinolinium ions with various allyl pinacolboronates are reported. The reactions are completely selective with respect to the site of the azinium ion that is attacked, to give various functionalized 1,4-dihydropyridines and 1,4-dihydroquinolines. Evidence suggests that the reactions proceed through nucleophilic allylgold(I) intermediates formed by transmetalation from allylboronates. Density functional theory (DFT) calculations provided mechanistic insight., (© 2022 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

ω-Unsaturated alcohols were "clipped" via alkene metathesis to a thioester activating group, which was followed by a chiral phosphoric acid catalyzed intramolecular oxa-Michael cyclization to yield tetrahydropyrans and spiro-tetrahydropyrans with excellent enantioselectivity. The mechanism and origin of the enantioselectivity was probed by DFT calculations and kinetic isotope studies, where there was excellent correlation between the computational and synthetic investigations.

The Minisci reaction is one of the most valuable methods for directly functionalizing basic heteroarenes to form carbon-carbon bonds. Use of prochiral, heteroatom-substituted radicals results in stereocenters being formed adjacent to the heteroaromatic system, generating motifs which are valuable in medicinal chemistry and chiral ligand design. Recently a highly enantioselective and regioselective protocol for the Minisci reaction was developed, using chiral phosphoric acid catalysis. However, the precise mechanism by which this process operated and the origin of selectivity remained unclear, making it challenging to develop the reaction more generally. Herein we report further experimental mechanistic studies which feed into detailed DFT calculations that probe the precise nature of the stereochemistry-determining step. Computational and experimental evidence together support Curtin-Hammett control in this reaction, with initial radical addition being quick and reversible, and enantioselectivity being achieved in the subsequent slower, irreversible deprotonation. A detailed survey via DFT calculations assessed a number of different possibilities for selectivity-determining deprotonation of the radical cation intermediate. Computations point to a clear preference for an initially unexpected mode of internal deprotonation enacted by the amide group, which is a crucial structural feature of the radical precursor, with the assistance of the associated chiral phosphate. This unconventional stereodetermining step underpins the high enantioselectivities and regioselectivities observed. The mechanistic model was further validated by applying it to a test set of substrates possessing varied structural features.

The development of an asymmetric "clip-cycle" synthesis of 2,2- and 3,3-disubstituted pyrrolidines and spiropyrrolidines, which are increasingly important scaffolds in drug discovery programs, is reported. Cbz-protected bis-homoallylic amines were activated by "clipping" them to thioacrylate via an alkene metathesis reaction. Enantioselective intramolecular aza-Michael cyclization onto the activated alkene, catalyzed by a chiral phosphoric acid, formed a pyrrolidine. The reaction accommodated a range of substitutions to form 2,2- and 3,3-disubstituted pyrrolidines and spiropyrrolidines with high enantioselectivities. The importance of the thioester activating group was demonstrated by comparison to ketone and oxoester-containing substrates. DFT studies supported the aza-Michael cyclization as the rate- and stereochemistry-determining step and correctly predicted the formation of the major enantiomer. The catalytic asymmetric syntheses of N -methylpyrrolidine alkaloids ( R )-irnidine and ( R )-bgugaine, which possess DNA binding and antibacterial properties, were achieved using the "clip-cycle" methodology.

Characterization of the complex molecular scaffold of the marine polyketide natural product phormidolide A represents a challenge that has persisted for nearly two decades. In light of discordant results arising from recent synthetic and biosynthetic reports, a rigorous study of the configuration of phormidolide A was necessary. This report outlines a synergistic effort employing computational and anisotropic NMR investigation, that provided orthogonal confirmation of the reassigned side chain, as well as supporting a further correction of the C7 stereocenter.

A robust system for automatic processing and assignment of raw 13 C and 1 H NMR data DP4-AI has been developed and integrated into our computational organic molecule structure elucidation workflow. Starting from a molecular structure with undefined stereochemistry or other structural uncertainty, this system allows for completely automated structure elucidation. Methods for NMR peak picking using objective model selection and algorithms for matching the calculated 13 C and 1 H NMR shifts to peaks in noisy experimental NMR data were developed. DP4-AI achieved a 60-fold increase in processing speed, and near-elimination of the need for scientist time, when rigorously evaluated using a challenging test set of molecules. DP4-AI represents a leap forward in NMR structure elucidation and a step-change in the functionality of DP4. It enables high-throughput analyses of databases and large sets of molecules, which were previously impossible, and paves the way for the discovery of new structural information through machine learning. This new functionality has been coupled with an intuitive GUI and is available as open-source software at https://github.com/KristapsE/DP4-AI., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

What computational methods should be used to achieve the most reliable result in computational structure elucidation? A study on the effect of quality and quantity of geometries on computational NMR structure elucidation performance is reported. Semi-empirical, HF and DFT methods were explored, and B3LYP optimized geometries in combination with mPW1PW91 shifts and M06-2X conformer energies was found to be best. The required number of conformers considered has also been investigated, as well as several methods for the reduction of this number. Clear guidelines for the best computational NMR structure elucidation methods for different levels of available computing power are provided.

A catalyst selection program, BINOPtimal, has been developed. This interactive web tool selects the best performing chiral phosphoric acid catalysts from analysis of the starting materials, imine and nucleophile, on the basis of rules derived from the transformations within its database. This procedure has been applied to an example transformation demonstrating the potential to assist reaction design. The tool is available at www-mmm.ch.cam.ac.uk.

We report a method for the direct and rapid conversion of primary and secondary alcohols to the corresponding phosphorothiolates in yields ranging from 64% to 97%, using as a coupling agent the iminium salt prepared from N,N-dimethylthioformamide and Meerwein's salt. Selective reaction of primary alcohols in the presence of secondary alcohols is possible. The reaction of secondary alcohols proceeds stereospecifically with inversion of configuration.

The origins of the stereodivergence in the thioester oxy-Michael cyclization for the formation of 4-hydroxy-2,6- cis - or 2,6- trans -substituted tetrahydropyran rings under different conditions was investigated both computationally and experimentally. Synthetic studies showed that the 4-hydroxyl group was essential for stereodivergence. When the 4-hydroxyl group was present, TBAF-mediated conditions gave the 2,6- trans -tetrahydropyran and trifluoroacetic acid-mediated conditions gave the 2,6- cis -tetrahydropyran. This stereodivergence vanished when the hydroxyl group was removed or protected. Computational studies revealed that: (i) the trifluoroacetic acid catalysed formation of 2,6- cis -tetrahydropyrans was mediated by a trifluoroacetate-hydroxonium bridge and proceeded via a chair-like transition state; (ii) the TBAF-mediated formation of 2,6- trans -tetrahydropyrans proceeded via a boat-like transition state, where the 4-hydroxyl group formed a crucial hydrogen bond to the cyclizing alkoxide; (iii) both reactions are under kinetic control. The utility of this stereodivergent approach for the formation of 4-hydroxy-2,6-substituted tetrahydropyran rings has been demonstrated by the total syntheses of the anti-osteoporotic natural products diospongin A and B.

The DP4 parameter, which provides a confidence level for NMR assignment, has been widely used to help assign the structures of many stereochemically-rich molecules. We present an improved version of the procedure, which can be downloaded as Python script instead of running within a web-browser, and which analyses output from open-source molecular modelling programs (TINKER and NWChem) in addition to being able to use output from commercial packages (Schrodinger's Macromodel and Jaguar; Gaussian). The new open-source workflow incorporates a method for the automatic generation of diastereomers using InChI strings and has been tested on a range of new structures. This improved workflow permits the rapid and convenient computational elucidation of structure and relative stereochemistry.

Marine toxins, which are produced by diverse marine organisms, can pose various threats to marine ecosystems and human health. Understanding their chemical structures and compositions is an important and challenging stage in the process of devising effective strategies for their management and reduction. Nuclear magnetic resonance (NMR) spectroscopy, alongside mass spectrometry, has emerged as the core and universal technique to achieve this task. This review highlights the role of NMR in obtaining structural data and information on marine toxins, and discusses the practical applications of NMR in the characterization of toxins. The study describes key NMR techniques, including one- and two-dimensional experiments, and discusses case studies of NMR implemented to tackle detection sensitivity and the complexities of specific toxins. Finally, the study analyzes how NMR methodologies may be advanced to improve the structural analysis of marine toxins. [ABSTRACT FROM AUTHOR]

In this work, inspired by the graph transformer, we presented an improved protocol, termed GT-NMR, which integrates 2D molecular graph representation with Transformer architecture, for accurate yet efficient prediction of NMR chemical shifts. The effectiveness of the GT-NMR was thoroughly examined with the standard nmrshiftdb2 dataset, 37 natural products and structural elucidation of 11 pairs of natural products. Systematical analysis affirms that GT-NMR outperforms traditional graph-based methods in all aspects, achieving state-of-the-art performance, with the mean absolute error of 0.158 and 1.189 ppm in predicting 1H and 13C NMR chemical shifts, respectively, for the standard nmrshiftdb2 dataset. Further scrutiny of its practical applications indicates that GT-NMR's efficacy is closely tied to molecular complexity, as quantified by the size-normalized spatial score (nSPS). For relatively simple molecules (nSPS < = 27.71), GT-NMR performs comparably to the best density functional while its effectiveness significantly diminishes with complex molecules characterized by higher nSPS values (nSPS > = 38.42). This trend is consistent across other graph-based NMR chemical shift prediction methods as well. Therefore, while employing GT-NMR or other graph-based methods for the rapid and routine prediction of NMR chemical shifts, it is advisable to utilize nSPS to assess their suitability. The source codes and trained model of GT-NMR are publicly available at GitHub. Scientific contribution GT-NMR, which combines the 2D molecular graph representation with the Transformer architecture, was implemented for the first time to predict atom-level NMR chemical shifts, achieving state-of-the-art performance. More importantly, the reliability of the GT-NMR and graph-based methods was assessed for the first time in terms of molecular complexity, as quantified by the size-normalized spacial score (nSPS). Systematical scrutiny demonstrated that GT-NMR offer a valuable way for routine application in structural screening and elucidation of relatively simple molecules. [ABSTRACT FROM AUTHOR]

This review focuses on the methodology used for the construction of tetrahydropyran (THP) rings in the synthesis of natural products over the last seven years. While methods like cyclisation onto oxocarbenium ions, reduction of cyclic hemi-ketals, Michael reactions, hetero-Diels-Alder cycloadditions and cyclisations onto epoxides continue to find application, several other strategies including metal-mediated cyclisations, ring-closing metathesis, radical cyclisations and carbocation cyclisations have also found use. This review is intended to provide an overview of the area for those who are unfamiliar, and to refresh and remind those who do work in the area of the exciting developments in the field.

A stereoselective synthesis of the C20-C32 tetrahydropyran core of the phorboxazoles has been achieved in only seven steps and in a 31% overall yield. The C22 epimer was also synthesized. The key step was a silyl ether deprotection/oxy-Michael cyclization. When this step was conducted under Brønsted acid conditions, the C20-C32 core was formed with the desired 2,6-cis-stereochemistry. However, when the silyl ether deprotection/oxy-Michael cyclization was conducted under fluoride conditions buffered with acetic acid, the C22 epimer of the core was the sole product.

The synthesis of biomimetic thioesters for enzymatic studies of ketoreductase (KR) domains from polyketide synthases is described. A TBS-protected dihydroxyalkene fragment was synthesised by a sequence involving a Nagao acetate aldol reaction, a Mukaiyama propionate aldol reaction, and a methylene Wittig olefination. Fragment coupling to N -acetylcysteamine (SNAC) (E)-3-hydroxyhex-4-enethioates by an olefin cross-metathesis (OCM) and subsequent deprotection gave the potential KR product stereoisomers. An analogous OCM with a SNAC (E)-3-ketohex-4-enethioate did not give the desired KR precursor, but the reaction could successfully be replaced by a Horner–Wadsworth–Emmons olefination between a SNAC 3-ketothioester phosphonate and a TBS-protected dihydroxy aldehyde. After deprotection, an intramolecular cyclisation was observed that needs to be considered as a spontaneous side reactivity in the enzymatic assays. [ABSTRACT FROM AUTHOR]

Inflammatory bowel disease (IBD) is a chronic, lifelong disorder characterized by inflammation of the gastrointestinal (GI) tract. The exact etiology of IBD remains incompletely understood due to its multifaceted nature, which includes genetic predisposition, environmental factors, and host immune response dysfunction. Currently, there is no cure for IBD. This review discusses the available treatment options and the challenges they present. Importantly, we examine emerging therapeutics, such as biologics and immunomodulators, that offer targeted treatment strategies for IBD. While many IBD patients do not respond adequately to most biologics, recent clinical trials combining biologics with small-molecule drugs (SMDs) have provided new insights into improving the IBD treatment landscape. Furthermore, numerous novel and specific therapeutic targets have been identified. The high cost of IBD drugs poses a significant barrier to treatment, but this challenge may be alleviated with the development of more affordable biosimilars. Additionally, emerging point-of-care protein biomarkers from serum and plasma are showing potential for enhancing the precision of IBD diagnosis and prognosis. Several natural products (NPs), including crude extracts, small molecules, and peptides, have demonstrated promising anti-inflammatory activity in high-throughput screening (HTS) systems and advanced artificial intelligence (AI)-assisted platforms, such as molecular docking and ADMET prediction. These platforms are advancing the search for alternative IBD therapies derived from natural sources, potentially leading to more affordable and safer treatment options with fewer side effects. [ABSTRACT FROM AUTHOR]

Structure elucidation is a stage of paramount importance in the discovery of novel compounds because molecular structure determines their physical, chemical and biological properties. Computational prediction of spectroscopic data, mainly NMR, has become a widely used tool to help in such tasks due to its increasing easiness and reliability. However, despite the continuous increment in CPU calculation power, classical quantum mechanics simulations still require a lot of effort. Accordingly, simulations of large or conformationally complex molecules are impractical. In this context, a growing number of research groups have explored the capabilities of machine learning (ML) algorithms in computational NMR prediction. In parallel, important advances have been made in the development of machine learninginspired methods to correlate the experimental and calculated NMR data to facilitate the structural elucidation process. Here, we have selected some essential papers to review this research area and propose conclusions and future perspectives for the field. [ABSTRACT FROM AUTHOR]

In addition to three known compounds (1 – 3), two new rearranged spongian diterpenes (4 and 5) with perhydroazulene and dioxabicyclooctane ring systems were isolated from the mantle and viscera of the Australian nudibranch G oniobranchus coi. The relative configuration of the major spiroepoxide 4 was explored by comparison with those of m -chloroperbenzoic acid oxidation products derived from dendrillolide A (1). Aldehydes 6 and 7 were identified as the ring-opened artefacts of the spiroepoxides 5 and 4 respectively, and yielded ketone 3 on storage. The relative configurations of lactols 8 and 9 , isolated as an inseparable mixture of diastereomers, were deduced by molecular modelling and computational studies. Acetylation of the lactol mixture provided dendrillolide A (1), further confirming the structural assignments of 8 and 9. Dissection of animal tissue established that the norditerpenoid metabolites were present in both mantle and viscera tissues. The nudibranch Goniobranchus coi sequesters and concentrates antifeedant oxygenated diterpenes into its mantle dermal formations to utilise as a chemical weapon when attacked by predators. Through chemical correlation, high-field NMR spectroscopy and molecular modelling new oxygenated metabolites were identified and elucidated. (Image credit: Louise C. Forster.) This article belongs to the collection 10th Anniversary Collection of RACI and AAS Award papers. [ABSTRACT FROM AUTHOR]

The application of quantum-based NMR methods for the structural elucidation of natural and unnatural products has grown significantly. However, accurately calculating the conformational landscape of flexible molecules with intricate intramolecular hydrogen bonding (IHB) networks continues to be a major challenge. In this work, we thoroughly studied the effect of entropic contributions (trough Gibbs free energies calculations) in the DP4+ performance. Our results show that to solve biased systems with strong IHB interactions requires computing the Boltzmann contributions using Gibbs free energies computed with at least triple-ξ basis set and SMD solvation model. In response to this finding, we have updated our DP4+App, a user-friendly Python applet that automates the entire process of calculating DP4+ probabilities. In the new version, the program allows for calculating of conformational contributions at any selected theory level, using either SCF or Gibbs free energies., (© 2024 John Wiley & Sons Ltd.)

Natural products (NPs) have played a vital role in human survival for millennia, particularly for their medicinal properties. Many traditional medicine practices continue to utilise crude plants and animal products for treating various diseases, including inflammation. In contrast, contemporary medicine focuses more on isolating drug-lead compounds from NPs to develop new and better treatment drugs for treating inflammatory disorders such as inflammatory bowel diseases. There is an ongoing search for new drug leads as there is still no cure for many inflammatory conditions. Various approaches and technologies are used in drug discoveries from NPs. This review comprehensively focuses on anti-inflammatory small molecules and describes the key strategies in identifying, extracting, fractionating and isolating small-molecule drug leads. This review also discusses the (i) most used approaches and recently available techniques, including artificial intelligence (AI), (ii) machine learning, and computational approaches in drug discovery; (iii) provides various animal models and cell lines used in in-vitro and in-vivo assessment of the anti-inflammatory potential of NPs. [ABSTRACT FROM AUTHOR]

The enantioselective Brønsted acid-catalyzed α-amidoalkylation reaction is a useful procedure is for the production of new drugs and natural products. In this context, Chiral Phosphoric Acid (CPA) catalysts are versatile catalysts for this type of reactions. The selection and design of new CPA catalysts for different enantioselective reactions has a dual interest because new CPA catalysts (tools) and chiral drugs or materials (products) can be obtained. However, this process is difficult and time consuming if approached from an experimental trial and error perspective. In this work, an Heuristic Perturbation-Theory and Machine Learning (HPTML) algorithm was used to seek a predictive model for CPA catalysts performance in terms of enantioselectivity in α-amidoalkylation reactions with R2 = 0.96 overall for training and validation series. It involved a Monte Carlo sampling of > 100,000 pairs of query and reference reactions. In addition, the computational and experimental investigation of a new set of intermolecular α-amidoalkylation reactions using BINOL-derived N-triflylphosphoramides as CPA catalysts is reported as a case of study. The model was implemented in a web server called MATEO: InterMolecular Amidoalkylation Theoretical Enantioselectivity Optimization, available online at: https://cptmltool.rnasa-imedir.com/CPTMLTools-Web/mateo. This new user-friendly online computational tool would enable sustainable optimization of reaction conditions that could lead to the design of new CPA catalysts along with new organic synthesis products. [ABSTRACT FROM AUTHOR]

Chiral tag molecular rotational resonance (MRR) spectroscopy is used to assign the absolute configuration of molecules that are chiral by virtue of deuterium substitution. Interest in the improved performance of deuterated active pharmaceutical ingredients has led to the development of precision deuteration reactions. These reactions often generate enantioisotopomer reaction products that pose challenges for chiral analysis. Chiral tag rotational spectroscopy uses noncovalent derivatization of the enantioisotopomer to create the diastereomers of the 1:1 molecular complexes of the analyte and a small, chiral molecule. Assignment of the absolute configuration requires high‐confidence determinations of the structures of these weakly bound complexes. A general search method, CREST, is used to identify candidate geometries. Subsequent geometry optimization using dispersion corrected density functional theory gives equilibrium geometries with sufficient accuracy to identify the isomers of the chiral tag complexes produced in the pulsed jet expansion used to introduce the sample into the MRR spectrometer. Rotational constant scaling based on the fact that the diastereomers have the same equilibrium geometry gives accurate predictions allowing identification of the homochiral and heterochiral tag complexes and, therefore, assignment of absolute configuration. The method is successfully applied to three oxygenated substrates from enantioselective Cu‐catalyzed alkene transfer hydrodeuteration reaction chemistry. [ABSTRACT FROM AUTHOR]

The structure of the sidechain crosslinked Tyr-Leu-Trp peptide produced by the biarylitide crosslinking cytochrome P450 Blt from Micromonospora sp. MW-13 has been reanalysed by a series of NMR, computational and isotope labelling experiments and shown to contain a C-N rather than a C-O bond. Additional in vivo experiments using such a modified peptide show there is a general tolerance of biarylitide crosslinking P450 enzymes for histidine to tryptophan mutations within their minimal peptide substrate sequences despite the lack of such residues noted in natural biarylitide gene clusters. This work further highlights the impressive ability of P450s from biarylitide biosynthesis pathways to act as biocatalysts for the formation of a range of sidechain crosslinked tripeptides., (© 2024 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Stereochemical determination of the flexible trinor-guaiane sesquiterpenoid, antheliol (1a) and the flexible diterpenoid, sangiangol B (2a), isolated from a marine soft coral, Anthelia sp., was supported by quantum chemical calculations of NMR chemical shifts at DFT levels. The relative configuration of antheliol is now revealed, as 1S*, 4S*, 7S*, 10R* as in 1b, whereas sangiangol B (2c) has complete stereochemistry as 1S*, 7R*, 8R*, 10R*, 11R*, 12S*. [ABSTRACT FROM AUTHOR]

The review covers research published since 2017 and is focused on enantioselective synthesis using radical reactions. It describes recent approaches to the asymmetric synthesis of chiral molecules based on the application of the metal catalysis, dual metal and organocatalysis and finally, pure organocatalysis including enzyme catalysis. This review focuses on the synthetic aspects of the methodology and tries to show which compounds can be obtained in enantiomerically enriched forms. [ABSTRACT FROM AUTHOR]

High‐temperature superconducting (HTS) materials have recently been incorporated into the construction of HTS cryogen‐free magnets for nuclear magnetic resonance (NMR) spectroscopy. These HTS NMR spectrometers do not require liquid cryogens, thereby providing significant cost savings and facilitating easy integration into chemistry laboratories. However, the optimal performance of these HTS magnets against standard cryogen NMR magnets must be evaluated, especially with demanding modern NMR applications such as NMR in anisotropic media. The stability of the HTS magnets over time and their performance with complex pulse sequence experiments are the main unknown factors of this new technology. In this study, we evaluate the utility of our prototype 400 MHz cryogen‐free power‐driven HTS NMR spectrometer, installed in the fumehood of a chemistry laboratory, for stereochemical analysis of three commercial natural products (artemisinin, artemether, and dihydroartemisinin) via measurement of anisotropic NMR data, in particular, residual dipolar couplings. The accuracy of measurement of the anisotropic NMR data with the HTS magnet spectrometer is evaluated through the CASE‐3D fitting protocol, as implemented in the Mestrenova‐StereoFitter software program. [ABSTRACT FROM AUTHOR]

The functionalisation of C–H bonds has been an enormous achievement in synthetic methodology, enabling new retrosynthetic disconnections and affording simple synthetic equivalents for synthons. Hydrogen atom transfer (HAT) is a key method for forming alkyl radicals from C–H substrates. Classic reactions, including the Barton nitrite ester reaction and Hofmann–Löffler–Freytag reaction, among others, provided early examples of HAT. However, recent developments in photoredox catalysis and electrochemistry have made HAT a powerful synthetic tool capable of introducing a wide range of functional groups into C–H bonds. Moreover, greater mechanistic insights into HAT have stimulated the development of increasingly site-selective protocols. Site-selectivity can be achieved through the tuning of electron density at certain C–H bonds using additives, a judicious choice of HAT reagent, and a solvent system. Herein, we describe the latest methods for functionalizing C–H/Si–H/Ge–H bonds using indirect HAT between 2018–2023, as well as a critical discussion of new HAT reagents, mechanistic aspects, substrate scopes, and background contexts of the protocols. [ABSTRACT FROM AUTHOR]

The use of quantum‐based NMR methods to complement and guide the connectivity and stereochemical assignment of natural and unnatural products has grown enormously. One of the unsolved problems is related to the improper calculation of the conformational landscape of flexible molecules that have functional groups capable of generating a complex network of intramolecular H‐bonding (IHB) interactions. Here the authors present MESSI (Multi‐Ensemble Strategy for Structural Identification), a method inspired by the wisdom of the crowd theory that breaks with the traditional mono‐ensemble approach. By including independent mappings of selected artificially manipulated ensembles, MESSI greatly improves the sense of the assignment by neutralizing potential energy biases. [ABSTRACT FROM AUTHOR]

The catalytic asymmetric inverse-electron-demand oxa-Diels–Alder (IODA) reaction is a highly effective synthetic method for creating enantioenriched six-membered oxygen-containing heterocycles. Despite significant effort in this area, simple α,β-unsaturated aldehydes/ketones and nonpolarized alkenes are seldom utilized as substrates due to their low reactivity and difficulties in achieving enantiocontrol. This report describes an intermolecular asymmetric IODA reaction between α-bromoacroleins and neutral alkenes that is catalyzed by oxazaborolidinium cation 1f. The resulting dihydropyrans are produced in high yields and excellent enantioselectivities over a broad range of substrates. The use of acrolein in the IODA reaction produces 3,4-dihydropyran with an unoccupied C6 position in the ring structure. This unique feature is utilized in the efficient synthesis of (+)-Centrolobine, demonstrating the practical synthetic utility of this reaction. Additionally, the study found that 2,6-trans-tetrahydropyran can undergo efficient epimerization into 2,6-cis-tetrahydropyran under Lewis acidic conditions. This structural core is widespread in natural products. The asymmetric inverse-electron-demand oxa-Diels–Alder reaction (IODA) between activated α,β-unsaturated carbonyl compounds with highly polarized alkenes has been reported before but acroleins or simple alkenes were so-far rarely employed as substrates. Here, the authors study the catalytic asymmetric intermolecular IODA reaction between acroleins and simple alkenes. [ABSTRACT FROM AUTHOR]

Recent strategies for enantioinduction often focus on employing a chiral catalyst to noncovalently interact with the substrate. By restricting the number of low energy diastereomeric transition states the reacting components can adopt, stereoselectivity can be achieved. Many of these noncovalent interactions include a significant dispersive component and these types of contacts have historically been difficult to model accurately. Modern computational methods have been designed to overcome such limitations. Using our computational work on chiral phosphate catalysis, we discuss the reasons for enantioselectivity in diverse reaction space. 1 Introduction 2 Chiral Phosphate Catalysis 3 Phosphate-Catalyzed Transfer Hydrogenation 4 Phosphate-Catalyzed Aza-Friedel–Crafts Reaction 5 Phosphate-Catalyzed Reactions Involving Allenamides 6 Comprehensive Qualitative Models 7 Chiral Phosphates and Thionium Intermediates 8 Conclusion [ABSTRACT FROM AUTHOR]

Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation. [ABSTRACT FROM AUTHOR]

A convenient regioselective synthesis of allyl- and vinylsilyl alcohols, from a common precursor, was described, by selecting the appropriate reaction conditions. Allyl- and vinylsilyl alcohols were tested in silyl-Prins cyclizations for the preparation of disubstituted oxygenated heterocycles in a one-pot sequential reaction. The methodology was sensitive to the structure of the starting alkenylsilyl alcohol and reaction conditions, with competitive pathways observed (particularly for allylsilyl alcohols), such as Peterson elimination and oxonia-Cope reactions. However, the use of vinylsilyl alcohols allowed the preparation of differently disubstituted cis-2,6-dihydropyrans in moderate to good yields. Computational studies support the proposed mechanism. [ABSTRACT FROM AUTHOR]

1′-N-Methylspiro[2′,11′′]indeno[1,2-b]quinoxalinespiro[3′,2]-6-arylmethylenecyclohexanone-4′-arylpyrrolidine compounds were synthesized by a catalyst-free one-pot two-step four-component [3+2] cycloaddition reaction of (2E,6E)-2,6-diarylidenecyclohexanone, ninhydrin hydrate, benzene-1,2-diamine and sarcosine. The structures of these products were characterized by a combinational analysis of NMR, IR, ESI-HRMS and X-ray data. [ABSTRACT FROM AUTHOR]

An Akaike Information Criterion (AIC) procedure (CASE-3D) has been successfully applied to the NMR based configurational assignment of reported hyacinthacines (1-3,5-8), recently target of configurational analysis using the popular DP4+ methodology. The present analysis makes use of reported 1 H and 13 C shifts and, in some particular cases, a few 3 J HH couplings. The difficulty in proper computational prediction of relative energies, in molecules capable of inter-molecular hydrogen bonding, introduces large errors in the prediction of conformationally averaged NMR properties in methods based on Boltzmann averaging such as DP4 or DP4+. In contrast CASE-3D conformational amplitudes are free parameters in the model. Here we show that the CASE-3D conformational model selection strategy, when combined with a larger energy cutoff in the molecular-modelling conformational exploration, was sufficient to correctly assign the relative configuration in five of seven cases. Introduction of more information, either by supplementing 1 H and 13 C data with a few J-couplings, or using a cutoff based on computed DFT energies for the definition of the conformational ensembles, allowed the safe assignment of configuration for all compounds., (© 2019 John Wiley & Sons, Ltd.)

Vibrational circular dichroism (VCD) spectroscopy can generate the data required for the assignment of absolute configuration, but the spectra are hard to interpret. We have recorded VCD data for thirty pairs of small organic compounds and we use this database to validate a method for the automated analysis of VCD spectra and the assignment of absolute configuration: the Cai•factor (Configuration: absolute information). The analysis of the data demonstrates that the procedure is a reliable and time-efficient method for determination of absolute configuration, which gives both the assignment and a measure of confidence in the outcome, even when the spectra are imperfect. The majority of molecules tested have a high confidence score and all of these have the correct assignment. [ABSTRACT FROM AUTHOR]

Density functional theory (DFT) benchmark studies of 1H and 13C NMR chemical shifts often yield differing conclusions, likely due to non-optimal test molecules and non-standardized data acquisition. To address this issue, we carefully selected and measured 1H and 13C NMR chemical shifts for 50 structurally diverse small organic molecules containing atoms from only the first two rows of the periodic table. Our NMR dataset, DELTA50, was used to calculate linear scaling factors and to evaluate the accuracy of 73 density functionals, 40 basis sets, 3 solvent models, and 3 gauge-referencing schemes. The best performing DFT methodologies for 1H and 13C NMR chemical shift predictions were WP04/6-311++G(2d,p) and ωB97X-D/def2-SVP, respectively, when combined with the polarizable continuum solvent model (PCM) and gauge-independent atomic orbital (GIAO) method. Geometries should be optimized at the B3LYP-D3/6-311G(d,p) level including the PCM solvent model for the best accuracy. Predictions of 20 organic compounds and natural products from a separate probe set had root-mean-square deviations (RMSD) of 0.07 to 0.19 for 1H and 0.5 to 2.9 for 13C. Maximum deviations were less than 0.5 and 6.5 ppm for 1H and 13C, respectively. [ABSTRACT FROM AUTHOR]

1H and 13C NMR chemical shifts of the tetrakis monoterpene indole alkaloid alasmontamine A, with a molecular formula of C84H91N8O12, have been calculated within the DFT framework. Six minimum energy conformers of this alkaloid were identified, and three key configurations that contribute to its NMR shielding constants were established. Several ambiguities in the reported assignment of the NMR chemical shifts of alasmontamine A have been resolved. [ABSTRACT FROM AUTHOR]

Hydrogen-bonding catalytic reactions have gained great interest. Herein, a hydrogen-bond-assisted three-component tandem reaction for the efficient synthesis of N-alkyl-4-quinolones is described. This novel strategy features the first proof of polyphosphate ester (PPE) as a dual hydrogen-bonding catalyst and the use of readily available starting materials for the preparation of N-alkyl-4-quinolones. The method provides a diversity of N-alkyl-4-quinolones in moderate to good yields. The compound 4h demonstrated good neuroprotective activity against N-methyl-ᴅ-aspartate (NMDA)-induced excitotoxicity in PC12 cells. [ABSTRACT FROM AUTHOR]

Through the lens of organocatalysis and phase transfer catalysis, we will examine the key components to calculate or predict catalysis-performance metrics, such as turnover frequency and measurement of stereoselectivity, via computational chemistry. The state-of-the-art tools available to calculate potential energy and, consequently, free energy, together with their caveats, will be discussed via examples from the literature. Through various examples from organocatalysis and phase transfer catalysis, we will highlight the challenges related to the mechanism, transition state theory, and solvation involved in translating calculated barriers to the turnover frequency or a metric of stereoselectivity. Examples in the literature that validated their theoretical models will be showcased. Lastly, the relevance and opportunity afforded by machine learning will be discussed. [ABSTRACT FROM AUTHOR]

Structural elucidation has always been challenging, and misassignment remains a stringent issue in the field of natural products. The growing interest in discovering unknown, complex natural structures accompanies the increasing awareness concerning misassignments in the community. The combination of various spectroscopic methods with molecular modeling has gained popularity in recent years. In this work, we demonstrated, for the first time, its power to fully elucidate the 2-dimensional and 3-dimensional structures of two epimers in an epimeric mixture of 6-hydroxyhippeastidine. DFT calculation of chemical shifts was first performed to assist the assignment of planar structures. Furthermore, relative and absolute configurations were established by three different ways of computer-assisted structure elucidation (CASE) coupled with ORD/ECD/VCD spectroscopies. In addition, the significant added value of OR/ORD computations to relative and absolute configuration determination was also revealed. Remarkably, the differentiation of two enantiomeric scaffolds (crinine and haemanthamine) was accomplished via OR/ORD calculations with cross-validation by ECD and VCD. [ABSTRACT FROM AUTHOR]